4WAB

Crystal structure of mPGES1 solved by native-SAD phasing

• PDB DOI: https://doi.org/10.2210/pdb4WAB/pdb

• Classification: ISOMERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2014-08-29 Released: 2014-12-10 
• Deposition Author(s): Weinert, T., Li, D., Howe, N., Caffrey, M., Wang, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.240 
• R-Value Work: 0.178 
• R-Value Observed: 0.181 

Literature

Fast native-SAD phasing for routine macromolecular structure determination.

Weinert, T., Olieric, V., Waltersperger, S., Panepucci, E., Chen, L., Zhang, H., Zhou, D., Rose, J., Ebihara, A., Kuramitsu, S., Li, D., Howe, N., Schnapp, G., Pautsch, A., Bargsten, K., Prota, A.E., Surana, P., Kottur, J., Nair, D.T., Basilico, F., Cecatiello, V., Pasqualato, S., Boland, A., Weichenrieder, O., Wang, B.C., Steinmetz, M.O., Caffrey, M., Wang, M.

(2015) Nat Methods 12: 131-133

• PubMed: 25506719 
• DOI: https://doi.org/10.1038/nmeth.3211
• Primary Citation of Related Structures:  
  4PGO, 4PII, 4R8T, 4R8U, 4TN8, 4TNO, 4WAB, 4WAU, 4WBQ, 4WBX


• PubMed Abstract: 
  

  We describe a data collection method that uses a single crystal to solve X-ray structures by native SAD (single-wavelength anomalous diffraction). We solved the structures of 11 real-life examples, including a human membrane protein, a protein-DNA complex and a 266-kDa multiprotein-ligand complex, using this method. The data collection strategy is suitable for routine structure determination and can be implemented at most macromolecular crystallography synchrotron beamlines.

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Organizational Affiliation: 

Swiss Light Source at Paul Scherrer Institut, Villigen, Switzerland.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 21.29 kDa 
• Atom Count: 1,358 
• Modelled Residue Count: 161 
• Deposited Residue Count: 178 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prostaglandin E synthase,Leukotriene C4 synthase	A	178	Homo sapiens	Mutation(s): 0  Gene Names: PTGES, MGST1L1, MPGES1, PGES, PIG12, LTC4S EC: 5.3.99.3 (PDB Primary Data), 1.11.1 (UniProt), 2.5.1 (UniProt), 4.4.1.20 (UniProt), 2.5.1.18 (UniProt) Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for O14684 (Homo sapiens) Explore O14684  Go to UniProtKB:  O14684
PHAROS:  O14684 GTEx:  ENSG00000148344
Find proteins for Q16873 (Homo sapiens) Explore Q16873  Go to UniProtKB:  Q16873
PHAROS:  Q16873
UniProt Groups	O14684Q16873

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LVJ	C [auth A]	2-[[2,6-bis(chloranyl)-3-[(2,2-dimethylpropanoylamino)methyl]phenyl]amino]-1-methyl-6-(2-methyl-2-oxidanyl-propoxy)-N-[2,2,2-tris(fluoranyl)ethyl]benzimidazole-5-carboxamide C27 H32 Cl2 F3 N5 O4 CHFOASGROVVRSK-UHFFFAOYSA-N
GSH	B [auth A]	GLUTATHIONE C10 H17 N3 O6 S RWSXRVCMGQZWBV-WDSKDSINSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.240 
• R-Value Work: 0.178 
• R-Value Observed: 0.181 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.72	α = 90
b = 86.72	β = 90
c = 180.36	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-10 
Deposition Author(s): Weinert, T., Li, D., Howe, N., Caffrey, M., Wang, M.

Revision History  

• Version 1.0: 2014-12-10
  Type: Initial release
  
• Version 1.1: 2014-12-31
  Changes: Database references
• Version 1.2: 2015-02-11
  Changes: Database references
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references